[med-svn] [Git][med-team/bioperl-run][master] 2 commits: fix hyphy test plan

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / bioperl-run


Commits:
3941c79b by Étienne Mollier at 2020-12-05T00:24:20+01:00
fix hyphy test plan

- - - - -
8fb5dd13 by Étienne Mollier at 2020-12-05T00:51:30+01:00
suppress retries for accessing remote Blast

- - - - -


3 changed files:

- debian/changelog
- debian/patches/hyphy.patch
- debian/patches/skip_tests_for_RemoteBlast.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -21,6 +21,8 @@ bioperl-run (1.7.3-5) UNRELEASED; urgency=medium
   * Add build time test dependencies to get BEDtools test data sets.
   * Add alternate-data.patch to use a dataset available in the Debian
     archive during build time testings.
+  * Suppress retries when attempting to access remote Blast resources,
+    this prevents hogging autopkgtest runners ten more minutes.
 
  -- Andreas Tille <tille at debian.org>  Thu, 03 Dec 2020 21:57:37 +0100
 


=====================================
debian/patches/hyphy.patch
=====================================
@@ -1,7 +1,7 @@
 Description: Hyphy
---- a/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
-+++ b/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
-@@ -236,7 +236,7 @@ sub run {
+--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
++++ bioperl-run/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
+@@ -236,7 +236,7 @@
  sub create_wrapper {
     my $self = shift;
  
@@ -10,18 +10,9 @@ Description: Hyphy
     $self->SUPER::create_wrapper($batchfile);
  }
  
---- a/t/Hyphy.t
-+++ b/t/Hyphy.t
-@@ -7,7 +7,7 @@ use strict;
- 
- BEGIN {
-     use Bio::Root::Test;
--    test_begin(-tests => 10,
-+    test_begin(-tests => 6,
-                -requires_module =>'IO::String');
- 
-     use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');
-@@ -59,10 +59,10 @@ SKIP: {
+--- bioperl-run.orig/t/Hyphy.t
++++ bioperl-run/t/Hyphy.t
+@@ -59,10 +59,10 @@
          if (($rc == 0) && ($debug == 1)){
              warn("ERROR in Modeltest module $rc:" . $modeltest->error_string() . "\n");
          }


=====================================
debian/patches/skip_tests_for_RemoteBlast.patch
=====================================
@@ -3,9 +3,9 @@ Author: Pranav Ballaney <ballaneypranav at gmail.com>
 Last-Update: 2020-04-05 
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/t/Tools/Run/RemoteBlast.t
-+++ b/t/Tools/Run/RemoteBlast.t
-@@ -7,7 +7,7 @@ BEGIN {
+--- bioperl-run.orig/t/Tools/Run/RemoteBlast.t
++++ bioperl-run/t/Tools/Run/RemoteBlast.t
+@@ -7,7 +7,7 @@
      use lib '.';
      use Bio::Root::Test;
  
@@ -14,7 +14,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
                 -requires_modules    => [qw(IO::String
                                             LWP
                                             LWP::UserAgent)],
-@@ -67,36 +67,36 @@ SKIP: {
+@@ -51,7 +51,7 @@
+     skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
+ 
+     diag("Retrieving $rids[0]...\n") if $v;
+-    my $max_attempts = 20;
++    my $max_attempts = 1;
+     my $rc;
+     while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
+         if ( !ref($rc) ) {
+@@ -67,36 +67,36 @@
          }
      }
  
@@ -81,7 +90,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  }
  
  SKIP: {
-@@ -146,36 +146,36 @@ SKIP: {
+@@ -130,7 +130,7 @@
+     skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
+ 
+     diag("waiting [$rids[0]]...") if $v;
+-    my $max_attempts = 20;
++    my $max_attempts = 1;
+     my $rc;
+     while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
+         if ( !ref($rc) ) {
+@@ -146,36 +146,36 @@
          }
      }
  
@@ -148,3 +166,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  }
  
  SKIP: {
+@@ -212,7 +212,7 @@
+ 
+     diag("waiting [$rids[0]]...") if $v;
+     # This blast usually takes 2x time compared to the other two
+-    my $max_attempts = 30;
++    my $max_attempts = 1;
+     my $rc;
+     while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
+         if ( !ref($rc) ) {



View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4...8fb5dd1322a5e4c97218898a12a9a1e4c2899fda

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4...8fb5dd1322a5e4c97218898a12a9a1e4c2899fda
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